Contacts of the strand formed by residues 115 - 122 (chain N) in PDB entry 6DZT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 115 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N VAL 3.8 1.0 - - - +
60N LYS* 3.6 1.6 - - - -
61N GLN* 2.8 48.8 + - + +
63N PRO* 6.2 2.0 - - + -
114N ALA* 1.3 73.7 - - - +
116N TYR* 1.3 62.8 + - - +
117N TYR* 3.8 31.6 + - + +
134N GLN 5.0 0.9 - - - +
135N GLY* 4.0 7.0 - - - -
136N THR 3.5 25.1 - - - +
137N SER* 4.8 12.8 - - - +
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Residues in contact with TYR 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N GLN* 2.8 21.9 + - - -
42N MET* 3.8 22.7 - - + -
58N TRP* 4.4 5.6 - - + -
59N VAL 3.4 2.5 - - - +
60N LYS* 3.9 30.6 + - + -
70N ILE* 3.6 31.0 - - + -
86N PHE* 5.5 1.3 - + - -
103N MET* 4.2 8.1 - - + -
105N LEU* 3.3 34.2 - - + +
112N ASP* 3.5 31.5 + - - -
114N ALA* 3.7 21.5 - - + -
115N VAL* 1.3 71.8 - - - +
117N TYR* 1.3 60.4 + - - +
135N GLY* 4.3 0.2 - - - -
136N THR* 3.3 18.2 + - - +
138N VAL* 4.1 22.2 - - + -
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Residues in contact with TYR 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N GLN* 4.0 3.8 - - - +
58N TRP* 3.3 10.2 - - - -
59N VAL* 2.9 38.2 + - + +
61N GLN* 2.3 49.3 + - + -
67N LEU* 4.3 8.1 - - + -
115N VAL* 3.8 21.6 - - + +
116N TYR* 1.3 73.5 - - - +
118N CYS* 1.3 60.9 + - - +
132N TRP* 3.6 30.5 - + + -
133N GLY 3.3 22.0 - - - +
134N GLN 3.9 11.7 - - - -
135N GLY* 3.8 7.2 - - - -
196N GLN* 2.9 14.7 + - - -
199N TRP 6.0 0.2 - - - -
200N LYS 3.9 3.3 + - - -
201N SER* 3.8 22.0 - - - -
202N PRO* 4.0 5.2 - - + -
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Residues in contact with CYS 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LEU* 3.5 10.9 - - - +
28N GLN* 3.8 23.8 + - - +
44N CYS* 2.0 48.2 - - - -
56N ILE* 4.1 2.9 - - + -
57N GLN 3.2 6.5 - - - +
58N TRP* 3.7 23.3 - - + -
117N TYR* 1.3 73.1 - - - +
119N ALA* 1.3 60.5 + - - +
132N TRP* 3.7 0.2 - - - -
133N GLY* 2.8 27.5 + - - +
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Residues in contact with ALA 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N LEU* 3.9 2.7 - - - -
56N ILE* 3.4 2.3 - - - -
57N GLN* 2.5 45.1 + - + +
59N VAL* 4.7 1.1 - - + -
117N TYR 4.2 0.4 + - - -
118N CYS* 1.3 75.6 - - - +
120N ARG* 1.3 61.9 + - - +
129N LEU* 3.7 36.8 - - + -
131N TYR 3.3 9.4 - - - +
132N TRP* 3.9 19.7 - - + +
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Residues in contact with ARG 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D GLU* 4.2 4.4 + - - -
24N VAL* 3.6 15.2 - - - +
26N LEU* 3.5 16.3 - - + +
49N TYR* 3.4 60.5 - - - +
54N TYR* 3.6 44.5 + - + -
55N THR 3.7 4.7 - - - +
56N ILE* 4.6 2.9 - - + +
119N ALA* 1.3 72.1 - - - +
121N LYS* 1.3 62.1 + - - +
129N LEU* 3.3 4.2 - - - -
130N ASP* 2.8 59.4 + - - +
131N TYR* 2.8 34.7 + - + +
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Residues in contact with LYS 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54N TYR* 3.5 4.6 - - - -
55N THR* 2.7 41.3 + - - +
57N GLN* 3.5 35.4 - - + +
119N ALA 3.8 0.2 + - - -
120N ARG* 1.3 77.3 - - - +
122N SER* 1.3 75.9 + - - +
123N SER 4.9 0.8 - - - -
124N ARG 3.1 19.2 + - - -
125N LEU* 4.8 3.6 + - - +
127N SER 3.4 16.9 + - - +
128N THR* 3.4 22.4 - - - +
129N LEU* 3.8 16.2 - - + -
130N ASP* 4.5 1.3 - - - -
249N HIS* 4.7 10.8 - - - -
254N TYR* 4.3 20.9 + - + -
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Residues in contact with SER 122 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C GLU* 4.2 6.9 + - - -
102D GLU* 3.7 15.4 + - - +
53N SER 4.6 1.2 + - - -
54N TYR* 3.6 28.3 - - - +
55N THR* 4.4 3.7 + - - +
121N LYS* 1.3 103.6 + - - +
123N SER* 1.3 68.9 + - - +
124N ARG* 3.2 21.0 + - - +
127N SER* 3.6 23.4 - - - -
128N THR 4.4 0.8 + - - -
130N ASP* 5.4 2.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il